It seems to me that QR codes could make it easy for someone to replace the original QR code with a different QR code at any place that accepts them and the merchant is none-the-wiser (unless there is some form of integration back to their PoS system) -- it seems like this could be a new form of skimming (stick your own QR code over any merchants :-)).

If most are screen based, you could just dynamically generate them and have them expire after N minutes. If someone wants a printed one make them jump through an application process for a long standing code.

They do for individual payments but storeowners sometimes tape their printed QR codes to walls and counters and they seem to want accommodate this use case too (essentially POS-less or "bring your own POS")